What is RADtool?

RADtool is a plugin for VMD that provides a range of options for the analysis and visualization/animation of ribosome structures. The primary purpose of RADtool is to provide a consistent approach for describing orientations of the small subunit (SSU) head and body domains. Over the last 20 years, these domains have been found to adopt many distinct orientations, which may be directly compared using RADtool.

Some capabilities of RADtool include:

• Calculation of Euler angles (rotation, tilt and tilt direction) of the SSU body and head domains
• Calculation of Euler-Rodrigues angles
• Support for ribosomes from bacteria, archaea and eukarya (mitochondrial and cytosolic)
• Graphical and command-line interfaces
• Automatic download and identification of the LSU and SSU
• Structure-based sequence alignment of the LSU and SSU to a reference E. coli structure
• Automated identification of structurally-conserved core regions (LSU, SSU body and SSU head)
• Many options to display and animate rotation, tilt and tilt direction for any ribosome structure
• Support for isolated SSUs, or LSU-SSU assemblies
• Support for alignment of isolated LSUs
• Support for analysis of simulated trajectories

Download RADtool

RADtool is a plugin for VMD. It has been tested with VMD v1.9.3 (on OSX, Linux and Windows) and pre-release versions of VMD 1.9.4. First download and install VMD, then download and launch RADtool. Configuration and usage instructions are available in the README file. We also provide short introductory videos on the Usage Examples Page.

Version	Release Date	md5 (.tgz or .zip file)
1.1	9/10/23
1.0 (.tgz)	6/23/22	95d0c8f7884af47e08d90780ef7b6976
1.0 (.zip)	6/23/22	0a23f9df8984418aa1abc5ee95ffb566
github

Page created and maintained by the Whitford Group at the Center for Theoretical Biological Physics, Northeastern University.